Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
Characterization of within-host Plasmodium falciparum diversity using next-generation sequence data.
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DOI：
10.1371/journal.pone.0032891
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Kwiatkowski DP
中科院分区：
文献类型：
--
作者：
Auburn S;Campino S;Miotto O;Djimde AA;Zongo I;Manske M;Maslen G;Mangano V;Alcock D;MacInnis B;Rockett KA;Clark TG;Doumbo OK;Ouédraogo JB;Kwiatkowski DP
我们对多克隆疟疾感染的组成和影响其多样性的流行病学因素的了解仍然很少。传统上，宿主内多样性是根据基于pcr的基因分型得出的感染多样性（MOI）来定义的。大规模并行的单分子测序技术现在可以在全基因组数据集上推导出个体读取计数，从而促进了新的统计方法的发展，以描述宿主内多样性。在这类测量中，FWS指标表征了宿主内多样性及其与种群水平多样性的关系。利用西非患者的恶性疟原虫现场分离株，我们在此探讨传统MOI和FWS方法之间的关系。FWS统计数据来自Illumina GA平台上测序的64个样品的86158个snp的读计数数据。msp-1和-2位点的MOI估计值通过PCR得到。两项指标之间存在显著相关性，尤其是msp-1位点（P = 5.92×10−5）。FWS度量应该比基于pcr的方法更健壮，因为它降低了对潜在位点特异性工件的敏感性。此外，FWS指标捕获了影响异交风险的一系列参数的信息，包括克隆数量（MOI）、它们的相对比例和遗传分化。这种方法应该为与宿主多样性相关并形成宿主多样性的因素提供新的见解。
Our understanding of the composition of multi-clonal malarial infections and the epidemiological factors which shape their diversity remain poorly understood. Traditionally within-host diversity has been defined in terms of the multiplicity of infection (MOI) derived by PCR-based genotyping. Massively parallel, single molecule sequencing technologies now enable individual read counts to be derived on genome-wide datasets facilitating the development of new statistical approaches to describe within-host diversity. In this class of measures the FWS metric characterizes within-host diversity and its relationship to population level diversity. Utilizing P. falciparum field isolates from patients in West Africa we here explore the relationship between the traditional MOI and FWS approaches. FWS statistics were derived from read count data at 86,158 SNPs in 64 samples sequenced on the Illumina GA platform. MOI estimates were derived by PCR at the msp-1 and -2 loci. Significant correlations were observed between the two measures, particularly with the msp-1 locus (P = 5.92×10−5). The FWS metric should be more robust than the PCR-based approach owing to reduced sensitivity to potential locus-specific artifacts. Furthermore the FWS metric captures information on a range of parameters which influence out-crossing risk including the number of clones (MOI), their relative proportions and genetic divergence. This approach should provide novel insights into the factors which correlate with, and shape within-host diversity.
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DOI：
10.1016/s0035-9203(99)90324-3
发表时间：
1999-02-01
影响因子：
2.2
作者：
Felger, I;Smith, T;Beck, HP
通讯作者：
Beck, HP
影响因子：
2.7
作者：
Engelbrecht, F;Tögel, E;Felger, I
通讯作者：
Felger, I
影响因子：
64.8
作者：
BOWCOCK, AM;RUIZLINARES, A;CAVALLISFORZA, LL
通讯作者：
CAVALLISFORZA, LL
DOI：
10.1073/pnas.0500078102
发表时间：
2005-05-24
影响因子：
11.1
作者：
de Roode, JC;Pansini, R;Read, AF
通讯作者：
Read, AF
影响因子：
2.7
作者：
Omumbo, JA;Guerra, CA;Hay, SI;Snow, RW
通讯作者：
Snow, RW